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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 28276f9 | Dave Tang | 2023-02-13 | Using ensembldb |
The ensembldb package can be used to retrieve genomic
and protein annotations and to map between protein, transcript, and
genome coordinates. This mapping relies on annotations of proteins
(their sequences) to their encoding transcripts which are stored in
EnsDb databases.
All functions, except
proteinToGenomeandtranscriptToGenomereturnIRangeswith negative coordinates if the mapping failed (e.g. because the identifier is unknown to the database, or if, for mappings to and from protein coordinates, the input coordinates are not within the coding region of a transcript).proteinToGenomeandtranscriptToGenomereturn emptyGRangesif mappings fail.
To begin, install the ensembldb and AnnotationHub packages.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!require("ensembldb", quietly = TRUE))
BiocManager::install("ensembldb")
if (!require("AnnotationHub", quietly = TRUE))
BiocManager::install("AnnotationHub")
library(ensembldb)
library(AnnotationHub)The AnnotationHub server provides easy R / Bioconductor access to large collections of publicly available whole genome resources, e.g,. ENSEMBL genome fasta or gtf files, UCSC chain resources, ENCODE data tracks at UCSC, etc.
Create an AnnotationHub object.
ah <- AnnotationHub(ask = FALSE)snapshotDate(): 2022-10-31Query.
ensdb_homo <- query(ah, c("EnsDb", "Homo sapiens"))
ensdb_homoAnnotationHub with 23 records
# snapshotDate(): 2022-10-31
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53211"]]'
title
AH53211 | Ensembl 87 EnsDb for Homo Sapiens
AH53715 | Ensembl 88 EnsDb for Homo Sapiens
AH56681 | Ensembl 89 EnsDb for Homo Sapiens
AH57757 | Ensembl 90 EnsDb for Homo Sapiens
AH60773 | Ensembl 91 EnsDb for Homo Sapiens
... ...
AH95744 | Ensembl 104 EnsDb for Homo sapiens
AH98047 | Ensembl 105 EnsDb for Homo sapiens
AH100643 | Ensembl 106 EnsDb for Homo sapiens
AH104864 | Ensembl 107 EnsDb for Homo sapiens
AH109336 | Ensembl 108 EnsDb for Homo sapiensLatest available Ensembl version.
latest <- nrow(mcols(ensdb_homo))
edb <- ensdb_homo[[latest]]loading from cacheedbEnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.7
|Creation time: Fri Oct 28 05:24:43 2022
|ensembl_version: 108
|ensembl_host: localhost
|Organism: Homo sapiens
|taxonomy_id: 9606
|genome_build: GRCh38
|DBSCHEMAVERSION: 2.2
| No. of genes: 70616.
| No. of transcripts: 275721.
|Protein data available.The
proteinToGenomefunction allows to map coordinates within the amino acid sequence of a protein to the corresponding DNA sequence on the genome. A protein identifier and the coordinates of the sequence within its amino acid sequence are required and have to be passed as anIRangesobject to the function. The protein identifier can either be passed as names of this object, or provided in a metadata column (mcols).
The example below (from the vignette) maps positions 5 to 9 within the amino acid sequence of the protein ENSP00000385415.
GAGE10_prt <- IRanges(start = 5, end = 9, names = "ENSP00000385415")
GAGE10_gnm <- proteinToGenome(GAGE10_prt, edb)Fetching CDS for 1 proteins ... 1 found
Checking CDS and protein sequence lengths ... 1/1 OKGAGE10_gnm$ENSP00000385415
GRanges object with 1 range and 7 metadata columns:
seqnames ranges strand | protein_id tx_id
<Rle> <IRanges> <Rle> | <character> <character>
[1] X 49304872-49304886 + | ENSP00000385415 ENST00000407599
exon_id exon_rank cds_ok protein_start protein_end
<character> <integer> <logical> <integer> <integer>
[1] ENSE00001692657 2 TRUE 5 9
-------
seqinfo: 1 sequence from GRCh38 genomeThe result is returned in a list, with one element for each range in
the input IRanges.
Below is an example with two proteins.
two_prt <- IRanges(
start = c(6, 15),
end = c(6, 15),
names = c("ENSP00000366863", "ENSP00000358262")
)
two_prt_to_gnm <- proteinToGenome(two_prt, edb)Fetching CDS for 2 proteins ... 2 found
Checking CDS and protein sequence lengths ... 2/2 OKtwo_prt_to_gnm$ENSP00000366863
GRanges object with 1 range and 7 metadata columns:
seqnames ranges strand | protein_id tx_id
<Rle> <IRanges> <Rle> | <character> <character>
[1] 13 75481750-75481752 - | ENSP00000366863 ENST00000377636
exon_id exon_rank cds_ok protein_start protein_end
<character> <integer> <logical> <integer> <integer>
[1] ENSE00003893703 1 TRUE 6 6
-------
seqinfo: 2 sequences from GRCh38 genome
$ENSP00000358262
GRanges object with 1 range and 7 metadata columns:
seqnames ranges strand | protein_id tx_id
<Rle> <IRanges> <Rle> | <character> <character>
[1] 1 147242746-147242748 + | ENSP00000358262 ENST00000369258
exon_id exon_rank cds_ok protein_start protein_end
<character> <integer> <logical> <integer> <integer>
[1] ENSE00003728289 1 TRUE 15 15
-------
seqinfo: 2 sequences from GRCh38 genomeWe use sapply() to convert the results into a data
frame.
get_pos <- function(x, add_chr = TRUE){
chr <- as.character(seqnames(x))
if(add_chr){
chr <- paste0("chr", chr)
}
list(
chr = chr,
start = start(x),
end = end(x)
)
}
as.data.frame(
t(sapply(two_prt_to_gnm, get_pos))
) chr start end
ENSP00000366863 chr13 75481750 75481752
ENSP00000358262 chr1 147242746 147242748
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] AnnotationHub_3.6.0 BiocFileCache_2.6.0 dbplyr_2.3.0
[4] ensembldb_2.22.0 AnnotationFilter_1.22.0 GenomicFeatures_1.50.4
[7] AnnotationDbi_1.60.0 Biobase_2.58.0 GenomicRanges_1.50.2
[10] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.1
[13] BiocGenerics_0.44.0 BiocManager_1.30.19 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.30.0 bitops_1.0-7
[3] matrixStats_0.63.0 fs_1.6.1
[5] bit64_4.0.5 filelock_1.0.2
[7] progress_1.2.2 httr_1.4.4
[9] rprojroot_2.0.3 tools_4.2.0
[11] bslib_0.4.2 utf8_1.2.3
[13] R6_2.5.1 lazyeval_0.2.2
[15] DBI_1.1.3 withr_2.5.0
[17] tidyselect_1.2.0 prettyunits_1.1.1
[19] processx_3.8.0 bit_4.0.5
[21] curl_5.0.0 compiler_4.2.0
[23] git2r_0.31.0 cli_3.6.0
[25] xml2_1.3.3 DelayedArray_0.24.0
[27] rtracklayer_1.58.0 sass_0.4.5
[29] callr_3.7.3 rappdirs_0.3.3
[31] stringr_1.5.0 digest_0.6.31
[33] Rsamtools_2.14.0 rmarkdown_2.20
[35] XVector_0.38.0 pkgconfig_2.0.3
[37] htmltools_0.5.4 MatrixGenerics_1.10.0
[39] fastmap_1.1.0 rlang_1.0.6
[41] rstudioapi_0.14 RSQLite_2.2.20
[43] shiny_1.7.4 jquerylib_0.1.4
[45] BiocIO_1.8.0 generics_0.1.3
[47] jsonlite_1.8.4 BiocParallel_1.32.5
[49] dplyr_1.1.0 RCurl_1.98-1.10
[51] magrittr_2.0.3 GenomeInfoDbData_1.2.9
[53] Matrix_1.5-3 Rcpp_1.0.10
[55] fansi_1.0.4 lifecycle_1.0.3
[57] stringi_1.7.12 whisker_0.4.1
[59] yaml_2.3.7 SummarizedExperiment_1.28.0
[61] zlibbioc_1.44.0 grid_4.2.0
[63] blob_1.2.3 parallel_4.2.0
[65] promises_1.2.0.1 crayon_1.5.2
[67] lattice_0.20-45 Biostrings_2.66.0
[69] hms_1.1.2 KEGGREST_1.38.0
[71] knitr_1.42 ps_1.7.2
[73] pillar_1.8.1 rjson_0.2.21
[75] codetools_0.2-18 biomaRt_2.54.0
[77] BiocVersion_3.16.0 XML_3.99-0.13
[79] glue_1.6.2 evaluate_0.20
[81] getPass_0.2-2 png_0.1-8
[83] vctrs_0.5.2 httpuv_1.6.8
[85] purrr_1.0.1 assertthat_0.2.1
[87] cachem_1.0.6 xfun_0.37
[89] mime_0.12 xtable_1.8-4
[91] restfulr_0.0.15 later_1.3.0
[93] tibble_3.1.8 GenomicAlignments_1.34.0
[95] memoise_2.0.1 interactiveDisplayBase_1.36.0
[97] ellipsis_0.3.2